Some people are too lazy or dim to read our critique of ENCODE (Graur D, Zheng Y, Price N, Azevedo RB, Zufall RA, Elhaik E. 2013. On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE. Genome Biol. Evol. 5:578-590) that clearly explains the two meanings of "function" and why the one used by ENCODE is wrong. To make it simple for them, I prepared a short presentation.

1. Interesting Questions:
1. What is “function”?

2. In Biology, there are two main concepts
of function:
• A historical concept of function, also
referred to as the “selected effect
function” or “proper function.”
• A non-historical concept of function,
also referred to as the “causal
function.”

3. • For a trait, A, to have a selected effect
function, F, it is necessary and (almost)
sufficient that the following two
conditions hold:
(1) A originated as a “reproduction” (a copy,
or a copy of a copy) of some prior entity
that performed F (or some function
similar to F) in the past.
(2) A exists because of this function.

4. • For a trait, A, to have a causal or non-
historical function, F, it is necessary and
sufficient that:
(1) A performs a function.

5. What is the function of the heart?
The proper
function is to pump
blood.
The causal functions of the heart are to add
300 grams to body weight, to produce
sounds, to be encased in the the
pericardium, to partially fill the
mediastinum, to provide an inaccurate logo
for Valentine Day cards, & to pump blood.

6. • Most biologists use the proper or
selected effect function.
• ENCODE used the causal function.
“Operationally, we define a functional element
as a discrete genome segment that encodes a
defined product (for example, protein or non-
coding RNA) or displays a reproducible
biochemical signature (for example, protein
binding, or a specific chromatin structure).”

7. • An example of a function that fits the
ENCODE definition: shoes binding
chewing gum. The function of shoe soles
is to bind sticky stuff in the summer.

8. “By the logic employed by ENCODE, following a
collision between a car and a pedestrian, a car’s
bonnet would be ascribed the 'function' of
projecting a pedestrian many meters and the
pedestrian would have the 'function' of deforming
the car’s bonnet.” Laurence Hurst 2013. BMC Biol. 11:58
Bonnet (UK) = Hood (USA)

9. Interesting Questions:
2. Why do people have “problems” with DNA that
has no function?

10. “… nothing is so alien to the
human mind as the idea of
randomness.”
John Cohen. 1960. Chance, Skill, and Luck: The
Psychology of Guessing and Gambling. Baltimore,
MD: Penguin Books.
Inability to deal with randomness

11. Apophenia /æpɵˈfiˈniə/
In psychology: the experience of seeing
meaningful patterns or connections in
random or meaningless data. A type of
mild or incipient schizophrenia.
In statistics, apophenia is known as Type I
error (false positives).
Klaus Conrad. 1958. Die beginnende Schizophrenie.
Versuch einer Gestaltanalyse des Wahns [Incipient
Schizophrenia: An Attempt to Analyze delusion].
Stuttgart: Georg Thieme Verlag.

14. Consider the term “junk DNA.” Implicit in this term is the
view that because the genome of an organism has been
cobbled together through a long, undirected
evolutionary process, the genome is a patchwork of
which only limited portions are essential to the
organism. Thus, on an evolutionary view we expect a
lot of useless DNA. If, on the other hand, organisms are
designed, we expect DNA, as much as possible, to
exhibit function.
Creationist William A. Dembski
Ideological/religious opposition

15. Junk = Heroin
“He's been hittin’ that junk, he's all fucked up”
Junk = Male genitalia
“Dude you just touched my junk!!... do it again
;)”
Semantic Baggage

16. Interesting Questions:
3. What is “junk”?

17. “Some years ago I noticed that there are two kinds of
rubbish in the world and that most languages have
different words to distinguish them. There is the rubbish
we keep, which is junk, and the rubbish we throw away,
which is garbage. The excess DNA in our genomes is
junk, and it is there because it is harmless, as well as
being useless, and because the molecular
processes generating extra DNA outpace
those getting rid of it.”
Sydney Brenner. 1998. Refuge of spandrels. Current Biology 8:R669.

18. “Were the extra DNA to become disadvantageous, it
would become subject to selection, just as junk that
takes up too much space, or is beginning to smell, is
instantly converted to garbage by one’s wife, that
excellent Darwinian instrument.”
Sydney Brenner. 1998. Refuge of spandrels. Current Biology 8:R669.

19. Graur’s garage: Functional, but full of junk A garage in which junk became garbage
A garage according to ENCODE. Such garages do not exist.